miga-base 0.7.10.0 → 0.7.12.2
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- checksums.yaml +4 -4
- data/lib/miga/cli/action/browse.rb +214 -0
- data/lib/miga/cli/action/browse/about.html +31 -0
- data/lib/miga/cli/action/browse/dataset.html +5 -0
- data/lib/miga/cli/action/browse/dataset_menu_item.html +3 -0
- data/lib/miga/cli/action/browse/datasets.html +4 -0
- data/lib/miga/cli/action/browse/favicon-32.png +0 -0
- data/lib/miga/cli/action/browse/index.html +8 -0
- data/lib/miga/cli/action/browse/layout.html +57 -0
- data/lib/miga/cli/action/browse/redirect.html +11 -0
- data/lib/miga/cli/action/browse/style.css +97 -0
- data/lib/miga/cli/action/derep_wf.rb +4 -0
- data/lib/miga/cli/action/stats.rb +1 -1
- data/lib/miga/cli/action/wf.rb +1 -0
- data/lib/miga/cli/base.rb +27 -26
- data/lib/miga/common/format.rb +26 -6
- data/lib/miga/daemon.rb +1 -1
- data/lib/miga/dataset/base.rb +2 -2
- data/lib/miga/dataset/result.rb +17 -13
- data/lib/miga/lair.rb +1 -1
- data/lib/miga/project/dataset.rb +3 -5
- data/lib/miga/result.rb +9 -7
- data/lib/miga/result/stats.rb +29 -11
- data/lib/miga/version.rb +2 -2
- data/scripts/cds.bash +0 -1
- data/test/project_test.rb +1 -1
- metadata +12 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: c57b841cc84841ebfd868af862204179e443d37eb4ec5550ea9ef7df63b9d933
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4
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+
data.tar.gz: 5512fe8305c2b6193f5d1a5c99e663ef480be32db2e8bdc7087826bdeeae5b35
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 63e095dded680c2a6d1519d8fc8788d4d44cf523fc84b9e67ee453dffb9f05c75e2acafc283b511f6b27638e678d53f7362b056f35d18d5b08893419c7d24302
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|
7
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+
data.tar.gz: efac7f7c3d65640b64dc6d9b32e3bd520faebda05a72f1b88a2ee4c11546b5366db1ac42ea296ba73fe1f7873244a9f64791a180c9094a374a7ebbf1c589d491
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@@ -0,0 +1,214 @@
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1
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+
# frozen_string_literal: true
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2
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+
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3
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+
require 'miga/cli/action'
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4
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+
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5
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# Action: miga browse
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6
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+
class MiGA::Cli::Action::Browse < MiGA::Cli::Action
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7
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+
def parse_cli
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8
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+
cli.parse do |opt|
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9
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cli.defaults = { open: true }
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10
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cli.opt_object(opt, [:project])
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11
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+
end
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12
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+
end
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13
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+
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14
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+
def perform
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15
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p = cli.load_project
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16
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create_empty_page(p)
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17
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generate_project_page(p)
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18
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say 'Creating dataset pages'
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19
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cli.load_project.each_dataset do |d|
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20
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generate_dataset_page(p, d)
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21
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end
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22
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generate_datasets_index(p)
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23
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say "Open in your browser: #{File.join(p.path, 'index.html')}"
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24
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end
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25
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+
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26
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private
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27
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+
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28
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##
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29
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# Create an empty page with necessary assets for project +p+
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30
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+
def create_empty_page(p)
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31
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say 'Creating project page'
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32
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+
FileUtils.mkdir_p(browse_file(p, '.'))
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33
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+
%w[favicon-32.png style.css].each do |i|
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34
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FileUtils.cp(template_file(i), browse_file(p, i))
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35
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+
end
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36
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+
write_file(p, 'about.html') do
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37
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build_from_template('about.html', citation: MiGA::MiGA.CITATION)
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38
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+
end
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39
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+
end
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40
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+
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41
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##
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42
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# Create landing page for project +p+
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43
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def generate_project_page(p)
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44
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# Redirect page
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45
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write_file(p, '../index.html') { build_from_template('redirect.html') }
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46
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+
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47
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# Summaries
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48
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+
summaries = Dir["#{p.path}/*.tsv"].map do |i|
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49
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+
b = File.basename(i)
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50
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"<li><a href='../#{b}'>#{b}</a></li>"
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51
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end.join('')
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52
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+
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53
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# Project index page
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54
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data = {
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55
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project_active: 'active',
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56
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information: format_metadata(p),
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57
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summaries: summaries.empty? ? 'None' : "<ul>#{summaries}</ul>",
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58
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results: format_results(p)
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59
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}
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60
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+
write_file(p, 'index.html') { build_from_template('index.html', data) }
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61
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end
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62
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+
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63
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##
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64
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# Create page for dataset +d+ within project +p+
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65
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def generate_dataset_page(p, d)
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66
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data = {
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67
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unmiga_name: d.name.unmiga_name,
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68
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information: format_metadata(d),
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69
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results: format_results(d)
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70
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}
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71
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write_file(p, "d_#{d.name}.html") do
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72
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build_from_template('dataset.html', data)
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73
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+
end
|
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74
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+
end
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75
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+
|
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76
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##
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77
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# Create pages for reference and query dataset indexes
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78
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def generate_datasets_index(p)
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79
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say 'Creating index pages'
|
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80
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+
data = format_dataset_index(p)
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81
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+
data.each do |k, v|
|
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82
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+
write_file(p, "#{k}_datasets.html") do
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83
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v[:list] = 'None' if v[:list] == ''
|
|
84
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build_from_template(
|
|
85
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'datasets.html',
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86
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v.merge(:"#{k}_datasets_active" => 'active')
|
|
87
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+
)
|
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88
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+
end
|
|
89
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+
end
|
|
90
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+
end
|
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91
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+
|
|
92
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+
def format_dataset_index(p)
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|
93
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data = {
|
|
94
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+
ref: { type_name: 'Reference', list: '' },
|
|
95
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+
qry: { type_name: 'Query', list: '' }
|
|
96
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+
}
|
|
97
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+
p.each_dataset do |d|
|
|
98
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+
data[d.ref? ? :ref : :qry][:list] +=
|
|
99
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+
"<li><a href='d_#{d.name}.html'>#{d.name.unmiga_name}</a></li>"
|
|
100
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+
end
|
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101
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+
data
|
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102
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+
end
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103
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+
|
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104
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##
|
|
105
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+
# Format +obj+ metadata as a table
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106
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+
def format_metadata(obj)
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107
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'<table class="table table-sm table-responsive">' +
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|
108
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+
obj.metadata.data.map do |k, v|
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109
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case k
|
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110
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+
when /^run_/, :plugins, :user
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111
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next
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112
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+
when :web_assembly_gz
|
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113
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v = "<a href='#{v}'>#{v[0..50]}...</a>"
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114
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+
when :datasets
|
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115
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v = v.size
|
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116
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+
end
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117
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"<tr><td class='text-right pr-4'><b>#{format_name(k)}</b></td>" \
|
|
118
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"<td>#{v}</td></tr>"
|
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119
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+
end.compact.join('') +
|
|
120
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+
'</table>'
|
|
121
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+
end
|
|
122
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+
|
|
123
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+
##
|
|
124
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+
# Format +obj+ results as cards
|
|
125
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+
def format_results(obj)
|
|
126
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+
o = ''
|
|
127
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+
obj.each_result do |key, res|
|
|
128
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+
links = format_result_links(res)
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|
129
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+
stats = format_result_stats(res)
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130
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next unless links || stats
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131
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name = format_name(key)
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132
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+
url_doc =
|
|
133
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+
'http://manual.microbial-genomes.org/part5/workflow#' +
|
|
134
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+
key.to_s.tr('_', '-')
|
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135
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+
o += <<~CARD
|
|
136
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+
<div class="col-md-6 mb-4">
|
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137
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<h3>#{name}</h3>
|
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138
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<div class='border-left p-3'>
|
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139
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#{stats}
|
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140
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#{links}
|
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141
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+
</div>
|
|
142
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+
<div class='border-top p-2 bg-light'>
|
|
143
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+
<a target=_blank href="#{url_doc}" class='p-2'>Learn more</a>
|
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144
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+
</div>
|
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145
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+
</div>
|
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146
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+
CARD
|
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147
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+
end
|
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148
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"<div class='row'>#{o}</div>"
|
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149
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+
end
|
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150
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+
|
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151
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+
def format_name(str)
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|
152
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+
str
|
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153
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.to_s.unmiga_name
|
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154
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+
.sub(/^./, &:upcase)
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155
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+
.gsub(/(Aai|Ani|Ogs|Cds|Ssu| db$| ssu )/, &:upcase)
|
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156
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+
.sub(/Haai/, 'hAAI')
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157
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+
.sub(/Mytaxa/, 'MyTaxa')
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158
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+
.sub(/ pvalue$/, ' p-value')
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159
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+
.sub(/contigs$/, 'Contigs')
|
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160
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+
end
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161
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+
|
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162
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+
def format_result_links(res)
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163
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+
links = []
|
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164
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+
res.each_file do |key, _|
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165
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+
name = format_name(key)
|
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166
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links << "<a href='../#{res.file_path(key, true)}'>#{name}</a><br/>"
|
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167
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+
end
|
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168
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+
links.empty? ? nil : links.join('')
|
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169
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+
end
|
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170
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+
|
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171
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def format_result_stats(res)
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172
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+
res.stats.map do |k, v|
|
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173
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+
v = [v, ''] unless v.is_a? Array
|
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174
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+
v[0] = ('%.3g' % v[0]) if v[0].is_a? Float
|
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175
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+
"<b>#{format_name(k)}:</b> #{v[0]}#{v[1]}<br/>"
|
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176
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+
end.join('') + '<br/>' unless res.stats.empty?
|
|
177
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+
end
|
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178
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+
|
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179
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##
|
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180
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# Write +file+ within the browse folder of project +p+ using the passed
|
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181
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# block output as content
|
|
182
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+
def write_file(p, file)
|
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183
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+
File.open(browse_file(p, file), 'w') { |fh| fh.print yield }
|
|
184
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+
end
|
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185
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+
|
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186
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+
##
|
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187
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+
# Use a +template+ file to generate content with a hash of +data+ over the
|
|
188
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+
# layout page if +layout+ is true
|
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189
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+
def build_from_template(template, data = {}, layout = true)
|
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190
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+
cont = File.read(template_file(template)).miga_variables(data)
|
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191
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+
return cont unless layout
|
|
192
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+
|
|
193
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build_from_template(
|
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194
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+
'layout.html',
|
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195
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+
data.merge(content: cont, project_name: cli.load_project.name),
|
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196
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false
|
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197
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)
|
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198
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+
end
|
|
199
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+
|
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200
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##
|
|
201
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# Path to the template browse file
|
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202
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+
def template_file(file)
|
|
203
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+
File.join(
|
|
204
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+
MiGA::MiGA.root_path,
|
|
205
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'lib', 'miga', 'cli', 'action', 'browse', file
|
|
206
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)
|
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207
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+
end
|
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208
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+
|
|
209
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##
|
|
210
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+
# Path to the browse file in the project
|
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211
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+
def browse_file(p, file)
|
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212
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File.join(p.path, 'browse', file)
|
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213
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+
end
|
|
214
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+
end
|
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@@ -0,0 +1,31 @@
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1
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<h1 class="h2 border-bottom pt-3 pb-2 mb-3">About MiGA</h1>
|
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2
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<p>
|
|
3
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MiGA is developed and maintained by
|
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4
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<a href='https://rodriguez-r.com/'>Luis M. Rodriguez-R</a>.
|
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5
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+
|
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6
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The MiGA codebase is
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7
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<a href='http://code.microbial-genomes.org/miga'>freely available</a> under the
|
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8
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+
terms of the terms of the
|
|
9
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<a href='http://code.microbial-genomes.org/miga/blob/master/LICENSE'>Artistic License 2.0</a>.
|
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10
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</p>
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11
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+
|
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12
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<p>
|
|
13
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MiGA is the result of a collaboration between the
|
|
14
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+
<a href='http://enve-omics.gatech.edu/'>Kostas Lab</a>
|
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15
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+
(<a href='http://www.gatech.edu/'>Georgia Institute of Technology</a>) and the
|
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16
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<a href='http://rdp.cme.msu.edu/'>RDP team</a>
|
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17
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+
(<a href='http://cme.msu.edu/'>Center for Microbial Ecology</a>,
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18
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<a href='https://msu.edu/'>Michigan State University</a>).
|
|
19
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The MiGA project is funded by the
|
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20
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+
<a href='http://nsf.gov/'>US National Science Foundation</a>
|
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21
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+
(Awards <a href='http://nsf.gov/awardsearch/showAward?AWD_ID=1356288'>#1356288</a> &
|
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22
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+
<a href='https://xras.xsede.org/public/requests/31162-XSEDE-MCB190042-1190572'>#MCB190042</a>).
|
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23
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</p>
|
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24
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+
|
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25
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<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Citation</h1>
|
|
26
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+
If you use MiGA in your work, consider citing:
|
|
27
|
+
<blockquote class='border-left p-3'>
|
|
28
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+
{{citation}}
|
|
29
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+
</blockquote>
|
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30
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+
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31
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Binary file
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@@ -0,0 +1,57 @@
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1
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<!doctype html>
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2
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<head>
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3
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<meta charset="utf-8">
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4
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+
<title>MiGA | {{project_name}}</title>
|
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5
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+
|
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6
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+
<!-- Remote assets -->
|
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7
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+
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/css/bootstrap.min.css" integrity="sha384-9aIt2nRpC12Uk9gS9baDl411NQApFmC26EwAOH8WgZl5MYYxFfc+NcPb1dKGj7Sk" crossorigin="anonymous">
|
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8
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+
<script src="https://code.jquery.com/jquery-3.5.1.slim.min.js" integrity="sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj" crossorigin="anonymous"></script>
|
|
9
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+
<script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js" integrity="sha384-Q6E9RHvbIyZFJoft+2mJbHaEWldlvI9IOYy5n3zV9zzTtmI3UksdQRVvoxMfooAo" crossorigin="anonymous"></script>
|
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10
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+
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/js/bootstrap.min.js" integrity="sha384-OgVRvuATP1z7JjHLkuOU7Xw704+h835Lr+6QL9UvYjZE3Ipu6Tp75j7Bh/kR0JKI" crossorigin="anonymous"></script>
|
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11
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+
|
|
12
|
+
<!-- Local assets -->
|
|
13
|
+
<link href="style.css" rel="stylesheet">
|
|
14
|
+
<link rel="icon" href="favicon-32.png" sizes="32x32" type="image/png">
|
|
15
|
+
</head>
|
|
16
|
+
<body>
|
|
17
|
+
<nav class="navbar navbar-dark sticky-top bg-dark flex-md-nowrap p-0 shadow">
|
|
18
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+
<a class="navbar-brand col-md-12 col-lg-12 mr-0 px-3"
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href="index.html">MiGA | {{project_name}}</a>
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type="button" data-toggle="collapse" data-target="#sidebarMenu"
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</li>
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href="ref_datasets.html">Reference datasets</a>
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</li>
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<a class="nav-link {{qry_datasets_active}}"
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href="qry_datasets.html">Query datasets</a>
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</li>
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href="about.html">About MiGA</a>
|
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</nav>
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<main role="main" class="col-md-9 ml-sm-auto col-lg-10 px-md-4">
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{{content}}
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</main>
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</div>
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</div>
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</body>
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@@ -0,0 +1,11 @@
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<!doctype html>
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<head>
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<title>MiGA Project</title>
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<meta http-equiv = "refresh" content = "1; url = browse/index.html" />
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</head>
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<body>
|
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<div style='font-size:200%; margin-top: 5em; text-align: center;'>
|
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Redirecting to <a href='browse/index.html'>Project page</a>...
|
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</div>
|
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</body>
|
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@@ -0,0 +1,97 @@
|
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body {
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font-size: .875rem;
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}
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/*
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* Sidebar
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*/
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.sidebar {
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position: fixed;
|
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top: 0;
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bottom: 0;
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left: 0;
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z-index: 100; /* Behind the navbar */
|
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padding: 48px 0 0; /* Height of navbar */
|
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box-shadow: inset -1px 0 0 rgba(0, 0, 0, .1);
|
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}
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@media (max-width: 767.98px) {
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.sidebar {
|
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top: 3rem;
|
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+
}
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|
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}
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|
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.sidebar-sticky {
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position: relative;
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top: 0;
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height: calc(100vh - 48px);
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padding-top: .5rem;
|
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overflow-x: hidden;
|
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overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
|
|
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|
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}
|
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|
+
|
|
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+
@supports ((position: -webkit-sticky) or (position: sticky)) {
|
|
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|
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.sidebar-sticky {
|
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position: -webkit-sticky;
|
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position: sticky;
|
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|
+
}
|
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|
+
}
|
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|
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.sidebar .nav-link {
|
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+
font-weight: 500;
|
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+
color: #333;
|
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+
}
|
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+
|
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+
.sidebar .nav-link .feather {
|
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+
margin-right: 4px;
|
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|
+
color: #999;
|
|
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+
}
|
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+
|
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+
.sidebar .nav-link.active {
|
|
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|
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color: #007bff;
|
|
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|
+
}
|
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|
+
|
|
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|
+
.sidebar .nav-link:hover .feather,
|
|
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|
+
.sidebar .nav-link.active .feather {
|
|
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|
+
color: inherit;
|
|
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|
+
}
|
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|
+
|
|
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|
+
.sidebar-heading {
|
|
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|
+
font-size: .75rem;
|
|
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|
+
text-transform: uppercase;
|
|
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|
+
}
|
|
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|
+
|
|
65
|
+
/*
|
|
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|
+
* Navbar
|
|
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|
+
*/
|
|
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|
+
|
|
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|
+
.navbar-brand {
|
|
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|
+
padding-top: .75rem;
|
|
71
|
+
padding-bottom: .75rem;
|
|
72
|
+
font-size: 1rem;
|
|
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|
+
background-color: rgba(0, 0, 0, .25);
|
|
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|
+
box-shadow: inset -1px 0 0 rgba(0, 0, 0, .25);
|
|
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|
+
}
|
|
76
|
+
|
|
77
|
+
.navbar .navbar-toggler {
|
|
78
|
+
top: .25rem;
|
|
79
|
+
right: 1rem;
|
|
80
|
+
}
|
|
81
|
+
|
|
82
|
+
.navbar .form-control {
|
|
83
|
+
padding: .75rem 1rem;
|
|
84
|
+
border-width: 0;
|
|
85
|
+
border-radius: 0;
|
|
86
|
+
}
|
|
87
|
+
|
|
88
|
+
.form-control-dark {
|
|
89
|
+
color: #fff;
|
|
90
|
+
background-color: rgba(255, 255, 255, .1);
|
|
91
|
+
border-color: rgba(255, 255, 255, .1);
|
|
92
|
+
}
|
|
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|
+
|
|
94
|
+
.form-control-dark:focus {
|
|
95
|
+
border-color: transparent;
|
|
96
|
+
box-shadow: 0 0 0 3px rgba(255, 255, 255, .25);
|
|
97
|
+
}
|
|
@@ -19,6 +19,10 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
|
|
|
19
19
|
'Use Average Amino Acid Identity (AAI) as genome similarity metric',
|
|
20
20
|
'By default: Use Average Nucleotide Identity (ANI)'
|
|
21
21
|
) { cli[:metric] = :aai }
|
|
22
|
+
opt.on(
|
|
23
|
+
'--ani',
|
|
24
|
+
'Use Average Nucleotide Identity (ANI) as similarity metric (default)'
|
|
25
|
+
) { cli[:metric] = :ani }
|
|
22
26
|
opt.on(
|
|
23
27
|
'--threshold FLOAT', Float,
|
|
24
28
|
"Metric threshold (%) to dereplicate. By default: #{cli[:threshold]}"
|
|
@@ -38,7 +38,7 @@ class MiGA::Cli::Action::Stats < MiGA::Cli::Action
|
|
|
38
38
|
end
|
|
39
39
|
if cli[:key].nil?
|
|
40
40
|
r[:stats].each do |k, v|
|
|
41
|
-
k_n = k
|
|
41
|
+
k_n = k.to_s.unmiga_name.sub(/^./, &:upcase)
|
|
42
42
|
cli.puts "#{k_n}: #{v.is_a?(Array) ? v.join(' ') : v}"
|
|
43
43
|
end
|
|
44
44
|
else
|
data/lib/miga/cli/action/wf.rb
CHANGED
data/lib/miga/cli/base.rb
CHANGED
|
@@ -11,39 +11,40 @@ module MiGA::Cli::Base
|
|
|
11
11
|
preproc_wf: 'Preprocess input genomes or metagenomes',
|
|
12
12
|
index_wf: 'Generate distance indexing of input genomes',
|
|
13
13
|
# Projects
|
|
14
|
-
new: '
|
|
15
|
-
about: '
|
|
16
|
-
doctor: '
|
|
17
|
-
get_db: '
|
|
14
|
+
new: 'Create an empty MiGA project',
|
|
15
|
+
about: 'Display information about a MiGA project',
|
|
16
|
+
doctor: 'Perform consistency checks on a MiGA project',
|
|
17
|
+
get_db: 'Download a pre-indexed database',
|
|
18
|
+
browse: 'Explore a project locally using a web browser',
|
|
18
19
|
# Datasets
|
|
19
|
-
add: '
|
|
20
|
-
get: '
|
|
21
|
-
ncbi_get: '
|
|
22
|
-
rm: '
|
|
23
|
-
find: '
|
|
20
|
+
add: 'Create a dataset in a MiGA project',
|
|
21
|
+
get: 'Download a dataset from public databases into a MiGA project',
|
|
22
|
+
ncbi_get: 'Download all genomes in a taxon from NCBI into a MiGA project',
|
|
23
|
+
rm: 'Remove a dataset from an MiGA project',
|
|
24
|
+
find: 'Find unregistered datasets based on result files',
|
|
24
25
|
ln: 'Link datasets (including results) from one project to another',
|
|
25
|
-
ls: '
|
|
26
|
-
archive: '
|
|
26
|
+
ls: 'List all registered datasets in an MiGA project',
|
|
27
|
+
archive: 'Generate a tar-ball with all files from select datasets',
|
|
27
28
|
# Results
|
|
28
|
-
add_result: '
|
|
29
|
-
stats: '
|
|
30
|
-
files: '
|
|
31
|
-
run: '
|
|
32
|
-
summary: '
|
|
33
|
-
next_step: '
|
|
29
|
+
add_result: 'Register a result',
|
|
30
|
+
stats: 'Extract statistics for the given result',
|
|
31
|
+
files: 'List registered files from the results of a dataset or project',
|
|
32
|
+
run: 'Execute locally one step analysis producing the given result',
|
|
33
|
+
summary: 'Generate a summary table for the statistics of all datasets',
|
|
34
|
+
next_step: 'Return the next task to run in a dataset or project',
|
|
34
35
|
# Objects (Datasets or Projects)
|
|
35
|
-
edit: '
|
|
36
|
+
edit: 'Edit the metadata of a dataset or project',
|
|
36
37
|
# System
|
|
37
38
|
init: 'Initialize MiGA to process new projects',
|
|
38
|
-
daemon: '
|
|
39
|
-
lair: '
|
|
40
|
-
date: '
|
|
41
|
-
console: '
|
|
39
|
+
daemon: 'Control the daemon of a MiGA project',
|
|
40
|
+
lair: 'Control groups of daemons for several MiGA projects',
|
|
41
|
+
date: 'Return the current date in standard MiGA format',
|
|
42
|
+
console: 'Open an IRB console with MiGA',
|
|
42
43
|
# Taxonomy
|
|
43
|
-
tax_set: '
|
|
44
|
-
tax_test: '
|
|
45
|
-
tax_index: '
|
|
46
|
-
tax_dist: '
|
|
44
|
+
tax_set: 'Register taxonomic information for datasets',
|
|
45
|
+
tax_test: 'Return test of taxonomic distributions for query datasets',
|
|
46
|
+
tax_index: 'Create a taxonomy-indexed list of the datasets',
|
|
47
|
+
tax_dist: 'Estimate distributions of distance by taxonomy',
|
|
47
48
|
}
|
|
48
49
|
|
|
49
50
|
@@TASK_ALIAS = {
|
data/lib/miga/common/format.rb
CHANGED
|
@@ -68,15 +68,20 @@ module MiGA::Common::Format
|
|
|
68
68
|
# a FastA or FastQ file (supports gzipped files). The +format+ must be a
|
|
69
69
|
# Symbol, one of +:fasta+ or +:fastq+. Additional estimations can be
|
|
70
70
|
# controlled via the +opts+ Hash. Supported options include:
|
|
71
|
-
# - +:n50+:
|
|
72
|
-
# - +:gc+:
|
|
73
|
-
# - +:x+:
|
|
71
|
+
# - +:n50+: Include the N50 and the median (in bp)
|
|
72
|
+
# - +:gc+: Include the G+C content (in %)
|
|
73
|
+
# - +:x+: Include the undetermined bases content (in %)
|
|
74
|
+
# - +:skew+: Include G-C and A-T sequence skew (in %; forces gc: true).
|
|
75
|
+
# See definition used here in DOI:10.1177/117693430700300006
|
|
74
76
|
def seqs_length(file, format, opts = {})
|
|
77
|
+
opts[:gc] = true if opts[:skew]
|
|
75
78
|
fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
|
|
76
79
|
l = []
|
|
77
80
|
gc = 0
|
|
78
81
|
xn = 0
|
|
79
|
-
|
|
82
|
+
t = 0
|
|
83
|
+
c = 0
|
|
84
|
+
i = 0 # <- Zlib::GzipReader doesn't set `$.`
|
|
80
85
|
fh.each_line do |ln|
|
|
81
86
|
i += 1
|
|
82
87
|
if (format == :fasta and ln =~ /^>/) or
|
|
@@ -86,6 +91,10 @@ module MiGA::Common::Format
|
|
|
86
91
|
l[l.size - 1] += ln.chomp.size
|
|
87
92
|
gc += ln.scan(/[GCgc]/).count if opts[:gc]
|
|
88
93
|
xn += ln.scan(/[XNxn]/).count if opts[:x]
|
|
94
|
+
if opts[:skew]
|
|
95
|
+
t += ln.scan(/[Tt]/).count
|
|
96
|
+
c += ln.scan(/[Cc]/).count
|
|
97
|
+
end
|
|
89
98
|
end
|
|
90
99
|
end
|
|
91
100
|
fh.close
|
|
@@ -97,6 +106,12 @@ module MiGA::Common::Format
|
|
|
97
106
|
o[:sd] = Math.sqrt o[:var]
|
|
98
107
|
o[:gc] = 100.0 * gc / o[:tot] if opts[:gc]
|
|
99
108
|
o[:x] = 100.0 * xn / o[:tot] if opts[:x]
|
|
109
|
+
if opts[:skew]
|
|
110
|
+
at = o[:tot] - gc
|
|
111
|
+
o[:at_skew] = 100.0 * (2 * t - at) / at
|
|
112
|
+
o[:gc_skew] = 100.0 * (2 * c - gc) / gc
|
|
113
|
+
end
|
|
114
|
+
|
|
100
115
|
if opts[:n50]
|
|
101
116
|
l.sort!
|
|
102
117
|
thr = o[:tot] / 2
|
|
@@ -132,9 +147,14 @@ class String
|
|
|
132
147
|
end
|
|
133
148
|
|
|
134
149
|
##
|
|
135
|
-
# Replace underscores by spaces or
|
|
150
|
+
# Replace underscores by spaces or other symbols depending on context
|
|
136
151
|
def unmiga_name
|
|
137
|
-
gsub(/_(str|sp|subsp|pv)__/, '_\\1._')
|
|
152
|
+
gsub(/_(str|sp|subsp|pv)__/, '_\\1._')
|
|
153
|
+
.gsub(/g_c_(content)/, 'G+C \\1')
|
|
154
|
+
.gsub(/g_c_(skew)/, 'G-C \\1')
|
|
155
|
+
.gsub(/a_t_(skew)/, 'A-T \\1')
|
|
156
|
+
.gsub(/x_content/, &:capitalize)
|
|
157
|
+
.tr('_', ' ')
|
|
138
158
|
end
|
|
139
159
|
|
|
140
160
|
##
|
data/lib/miga/daemon.rb
CHANGED
|
@@ -185,7 +185,7 @@ class MiGA::Daemon < MiGA::MiGA
|
|
|
185
185
|
return if project.dataset_names.empty?
|
|
186
186
|
|
|
187
187
|
# Double-check if all datasets are ready
|
|
188
|
-
return unless project.done_preprocessing?
|
|
188
|
+
return unless project.done_preprocessing?
|
|
189
189
|
|
|
190
190
|
# Queue project-level job
|
|
191
191
|
to_run = project.next_task(nil, false)
|
data/lib/miga/dataset/base.rb
CHANGED
|
@@ -66,7 +66,7 @@ module MiGA::Dataset::Base
|
|
|
66
66
|
@@PREPROCESSING_TASKS = [
|
|
67
67
|
:raw_reads, :trimmed_reads, :read_quality, :trimmed_fasta,
|
|
68
68
|
:assembly, :cds, :essential_genes, :ssu, :mytaxa, :mytaxa_scan,
|
|
69
|
-
:
|
|
69
|
+
:taxonomy, :distances, :stats
|
|
70
70
|
]
|
|
71
71
|
|
|
72
72
|
##
|
|
@@ -77,7 +77,7 @@ module MiGA::Dataset::Base
|
|
|
77
77
|
##
|
|
78
78
|
# Tasks to be executed only in datasets that are not multi-organism. These
|
|
79
79
|
# tasks are ignored for multi-organism datasets or for unknown types.
|
|
80
|
-
@@ONLY_NONMULTI_TASKS = [:mytaxa_scan, :
|
|
80
|
+
@@ONLY_NONMULTI_TASKS = [:mytaxa_scan, :taxonomy, :distances]
|
|
81
81
|
@@_ONLY_NONMULTI_TASKS_H = Hash[@@ONLY_NONMULTI_TASKS.map { |i| [i, true] }]
|
|
82
82
|
|
|
83
83
|
##
|
data/lib/miga/dataset/result.rb
CHANGED
|
@@ -26,15 +26,24 @@ module MiGA::Dataset::Result
|
|
|
26
26
|
# The values are symbols:
|
|
27
27
|
# - empty: the dataset has no data
|
|
28
28
|
# - inactive: the dataset is inactive
|
|
29
|
+
# - upstream: the task is upstream from dataset's input
|
|
29
30
|
# - force: forced to ignore by metadata
|
|
30
31
|
# - project: incompatible project
|
|
31
32
|
# - noref: incompatible dataset, only for reference
|
|
32
33
|
# - multi: incompatible dataset, only for multi
|
|
33
34
|
# - nonmulti: incompatible dataset, only for nonmulti
|
|
35
|
+
# - complete: the task is already complete
|
|
34
36
|
# - execute: do not ignore, execute the task
|
|
35
37
|
def why_ignore(task)
|
|
36
|
-
if !
|
|
38
|
+
if !get_result(task).nil?
|
|
39
|
+
:complete
|
|
40
|
+
elsif !active?
|
|
37
41
|
:inactive
|
|
42
|
+
elsif first_preprocessing.nil?
|
|
43
|
+
:empty
|
|
44
|
+
elsif @@PREPROCESSING_TASKS.index(task) <
|
|
45
|
+
@@PREPROCESSING_TASKS.index(first_preprocessing)
|
|
46
|
+
:upstream
|
|
38
47
|
elsif !metadata["run_#{task}"].nil?
|
|
39
48
|
metadata["run_#{task}"] ? :execute : :force
|
|
40
49
|
elsif task == :taxonomy && project.metadata[:ref_project].nil?
|
|
@@ -56,7 +65,7 @@ module MiGA::Dataset::Result
|
|
|
56
65
|
# initial input. Passes +save+ to #add_result.
|
|
57
66
|
def first_preprocessing(save = false)
|
|
58
67
|
@first_processing ||= @@PREPROCESSING_TASKS.find do |t|
|
|
59
|
-
!
|
|
68
|
+
!add_result(t, save).nil?
|
|
60
69
|
end
|
|
61
70
|
end
|
|
62
71
|
|
|
@@ -121,17 +130,12 @@ module MiGA::Dataset::Result
|
|
|
121
130
|
# - complete: a task with registered results
|
|
122
131
|
# - pending: a task queued to be performed
|
|
123
132
|
def result_status(task)
|
|
124
|
-
|
|
125
|
-
|
|
126
|
-
|
|
127
|
-
|
|
128
|
-
|
|
129
|
-
|
|
130
|
-
:-
|
|
131
|
-
elsif ignore_task?(task)
|
|
132
|
-
:"ignore_#{why_ignore task}"
|
|
133
|
-
else
|
|
134
|
-
:pending
|
|
133
|
+
reason = why_ignore(task)
|
|
134
|
+
case reason
|
|
135
|
+
when :upstream; :-
|
|
136
|
+
when :execute; :pending
|
|
137
|
+
when :complete; :complete
|
|
138
|
+
else; :"ignore_#{reason}"
|
|
135
139
|
end
|
|
136
140
|
end
|
|
137
141
|
|
data/lib/miga/lair.rb
CHANGED
data/lib/miga/project/dataset.rb
CHANGED
|
@@ -134,12 +134,10 @@ module MiGA::Project::Dataset
|
|
|
134
134
|
##
|
|
135
135
|
# Are all the datasets in the project preprocessed? Save intermediate results
|
|
136
136
|
# if +save+ (until the first incomplete dataset is reached).
|
|
137
|
-
def done_preprocessing?(save =
|
|
138
|
-
|
|
139
|
-
|
|
140
|
-
return false if ds.is_ref? and not ds.done_preprocessing?(save)
|
|
137
|
+
def done_preprocessing?(save = false)
|
|
138
|
+
!each_dataset.any? do |d|
|
|
139
|
+
d.ref? && d.active? && !d.done_preprocessing?(save)
|
|
141
140
|
end
|
|
142
|
-
true
|
|
143
141
|
end
|
|
144
142
|
|
|
145
143
|
##
|
data/lib/miga/result.rb
CHANGED
|
@@ -81,20 +81,22 @@ class MiGA::Result < MiGA::MiGA
|
|
|
81
81
|
end
|
|
82
82
|
|
|
83
83
|
##
|
|
84
|
-
# Directory containing the result
|
|
85
|
-
|
|
86
|
-
|
|
84
|
+
# Directory containing the result; by default an absolute path, if
|
|
85
|
+
# +relative+ is true returns the path relative to the parent project
|
|
86
|
+
def dir(relative = false)
|
|
87
|
+
relative ? relative_dir : File.dirname(path)
|
|
87
88
|
end
|
|
88
89
|
|
|
89
90
|
##
|
|
90
|
-
# Absolute path to the file(s) defined by symbol +k
|
|
91
|
-
|
|
91
|
+
# Absolute path to the file(s) defined by symbol +k+, or relative
|
|
92
|
+
# path if +relative+ is true
|
|
93
|
+
def file_path(k, relative = false)
|
|
92
94
|
k = k.to_sym
|
|
93
95
|
f = self[:files].nil? ? nil : self[:files][k]
|
|
94
96
|
return nil if f.nil?
|
|
95
|
-
return File.
|
|
97
|
+
return File.join(dir(relative), f) unless f.is_a? Array
|
|
96
98
|
|
|
97
|
-
f.map { |fi| File.
|
|
99
|
+
f.map { |fi| File.join(dir(relative), fi) }
|
|
98
100
|
end
|
|
99
101
|
|
|
100
102
|
##
|
data/lib/miga/result/stats.rb
CHANGED
|
@@ -17,32 +17,45 @@ module MiGA::Result::Stats
|
|
|
17
17
|
self[:stats]
|
|
18
18
|
end
|
|
19
19
|
|
|
20
|
+
##
|
|
21
|
+
# Access the stats entry of results
|
|
22
|
+
def stats
|
|
23
|
+
self[:stats]
|
|
24
|
+
end
|
|
25
|
+
|
|
20
26
|
private
|
|
21
27
|
|
|
22
28
|
def compute_stats_raw_reads
|
|
23
29
|
stats = {}
|
|
30
|
+
seq_opts = { gc: true, x: true, skew: true }
|
|
24
31
|
if self[:files][:pair1].nil?
|
|
25
|
-
s = MiGA::MiGA.seqs_length(file_path(:single), :fastq,
|
|
32
|
+
s = MiGA::MiGA.seqs_length(file_path(:single), :fastq, seq_opts)
|
|
26
33
|
stats = {
|
|
27
34
|
reads: s[:n],
|
|
28
35
|
length_average: [s[:avg], 'bp'],
|
|
29
36
|
length_standard_deviation: [s[:sd], 'bp'],
|
|
30
37
|
g_c_content: [s[:gc], '%'],
|
|
31
|
-
x_content: [s[:x], '%']
|
|
38
|
+
x_content: [s[:x], '%'],
|
|
39
|
+
g_c_skew: [s[:gc_skew], '%'],
|
|
40
|
+
a_t_skew: [s[:at_skew], '%']
|
|
32
41
|
}
|
|
33
42
|
else
|
|
34
|
-
s1 = MiGA::MiGA.seqs_length(file_path(:pair1), :fastq,
|
|
35
|
-
s2 = MiGA::MiGA.seqs_length(file_path(:pair2), :fastq,
|
|
43
|
+
s1 = MiGA::MiGA.seqs_length(file_path(:pair1), :fastq, seq_opts)
|
|
44
|
+
s2 = MiGA::MiGA.seqs_length(file_path(:pair2), :fastq, seq_opts)
|
|
36
45
|
stats = {
|
|
37
46
|
read_pairs: s1[:n],
|
|
38
47
|
forward_length_average: [s1[:avg], 'bp'],
|
|
39
48
|
forward_length_standard_deviation: [s1[:sd], 'bp'],
|
|
40
49
|
forward_g_c_content: [s1[:gc], '%'],
|
|
41
50
|
forward_x_content: [s1[:x], '%'],
|
|
51
|
+
forward_g_c_skew: [s1[:gc_skew], '%'],
|
|
52
|
+
forward_a_t_skew: [s1[:at_skew], '%'],
|
|
42
53
|
reverse_length_average: [s2[:avg], 'bp'],
|
|
43
54
|
reverse_length_standard_deviation: [s2[:sd], 'bp'],
|
|
44
55
|
reverse_g_c_content: [s2[:gc], '%'],
|
|
45
|
-
reverse_x_content: [s2[:x], '%']
|
|
56
|
+
reverse_x_content: [s2[:x], '%'],
|
|
57
|
+
reverse_g_c_skew: [s2[:gc_skew], '%'],
|
|
58
|
+
reverse_a_t_skew: [s2[:at_skew], '%']
|
|
46
59
|
}
|
|
47
60
|
end
|
|
48
61
|
stats
|
|
@@ -50,19 +63,22 @@ module MiGA::Result::Stats
|
|
|
50
63
|
|
|
51
64
|
def compute_stats_trimmed_fasta
|
|
52
65
|
f = self[:files][:coupled].nil? ? file_path(:single) : file_path(:coupled)
|
|
53
|
-
s = MiGA::MiGA.seqs_length(f, :fasta, gc: true, x: true)
|
|
66
|
+
s = MiGA::MiGA.seqs_length(f, :fasta, gc: true, x: true, skew: true)
|
|
54
67
|
{
|
|
55
68
|
reads: s[:n],
|
|
56
69
|
length_average: [s[:avg], 'bp'],
|
|
57
70
|
length_standard_deviation: [s[:sd], 'bp'],
|
|
58
71
|
g_c_content: [s[:gc], '%'],
|
|
59
|
-
x_content: [s[:x], '%']
|
|
72
|
+
x_content: [s[:x], '%'],
|
|
73
|
+
g_c_skew: [s[:gc_skew], '%'],
|
|
74
|
+
a_t_skew: [s[:at_skew], '%']
|
|
60
75
|
}
|
|
61
76
|
end
|
|
62
77
|
|
|
63
78
|
def compute_stats_assembly
|
|
64
79
|
s = MiGA::MiGA.seqs_length(
|
|
65
|
-
file_path(:largecontigs), :fasta,
|
|
80
|
+
file_path(:largecontigs), :fasta,
|
|
81
|
+
n50: true, gc: true, x: true, skew: true
|
|
66
82
|
)
|
|
67
83
|
{
|
|
68
84
|
contigs: s[:n],
|
|
@@ -70,7 +86,9 @@ module MiGA::Result::Stats
|
|
|
70
86
|
total_length: [s[:tot], 'bp'],
|
|
71
87
|
longest_sequence: [s[:max], 'bp'],
|
|
72
88
|
g_c_content: [s[:gc], '%'],
|
|
73
|
-
x_content: [s[:x], '%']
|
|
89
|
+
x_content: [s[:x], '%'],
|
|
90
|
+
g_c_skew: [s[:gc_skew], '%'],
|
|
91
|
+
a_t_skew: [s[:at_skew], '%']
|
|
74
92
|
}
|
|
75
93
|
end
|
|
76
94
|
|
|
@@ -133,9 +151,9 @@ module MiGA::Result::Stats
|
|
|
133
151
|
source.save
|
|
134
152
|
|
|
135
153
|
# Inactivate low-quality datasets
|
|
136
|
-
min_qual = (project.metadata[:min_qual] ||
|
|
154
|
+
min_qual = (project.metadata[:min_qual] || 25)
|
|
137
155
|
if min_qual != 'no' && stats[:quality] < min_qual
|
|
138
|
-
source.inactivate! 'Low genome
|
|
156
|
+
source.inactivate! 'Low quality genome'
|
|
139
157
|
end
|
|
140
158
|
end
|
|
141
159
|
stats
|
data/lib/miga/version.rb
CHANGED
|
@@ -8,7 +8,7 @@ module MiGA
|
|
|
8
8
|
# - Float representing the major.minor version.
|
|
9
9
|
# - Integer representing gem releases of the current version.
|
|
10
10
|
# - Integer representing minor changes that require new version number.
|
|
11
|
-
VERSION = [0.7,
|
|
11
|
+
VERSION = [0.7, 12, 2]
|
|
12
12
|
|
|
13
13
|
##
|
|
14
14
|
# Nickname for the current major.minor version.
|
|
@@ -16,7 +16,7 @@ module MiGA
|
|
|
16
16
|
|
|
17
17
|
##
|
|
18
18
|
# Date of the current gem release.
|
|
19
|
-
VERSION_DATE = Date.new(2020,
|
|
19
|
+
VERSION_DATE = Date.new(2020, 7, 24)
|
|
20
20
|
|
|
21
21
|
##
|
|
22
22
|
# Reference of MiGA.
|
data/scripts/cds.bash
CHANGED
|
@@ -20,7 +20,6 @@ fi
|
|
|
20
20
|
TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" -m type | cut -f 2)
|
|
21
21
|
case "$TYPE" in
|
|
22
22
|
metagenome|virome)
|
|
23
|
-
$CMD -p meta
|
|
24
23
|
prodigal -a "${DATASET}.faa" -d "${DATASET}.fna" -o "${DATASET}.gff3" \
|
|
25
24
|
-f gff -q -i "../05.assembly/${DATASET}.LargeContigs.fna" -p meta
|
|
26
25
|
;;
|
data/test/project_test.rb
CHANGED
|
@@ -108,7 +108,7 @@ class ProjectTest < Test::Unit::TestCase
|
|
|
108
108
|
d1 = p1.add_dataset('BAH')
|
|
109
109
|
assert_not_predicate(p1, :done_preprocessing?)
|
|
110
110
|
FileUtils.touch(File.join(p1.path, 'data', '90.stats', "#{d1.name}.done"))
|
|
111
|
-
|
|
111
|
+
assert { p1.done_preprocessing? true }
|
|
112
112
|
assert_nil(p1.next_inclade)
|
|
113
113
|
p1.metadata[:type] = :clade
|
|
114
114
|
assert_equal(:subclades, p1.next_inclade)
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: miga-base
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.7.
|
|
4
|
+
version: 0.7.12.2
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Luis M. Rodriguez-R
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2020-
|
|
11
|
+
date: 2020-07-24 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: daemons
|
|
@@ -118,6 +118,16 @@ files:
|
|
|
118
118
|
- lib/miga/cli/action/add.rb
|
|
119
119
|
- lib/miga/cli/action/add_result.rb
|
|
120
120
|
- lib/miga/cli/action/archive.rb
|
|
121
|
+
- lib/miga/cli/action/browse.rb
|
|
122
|
+
- lib/miga/cli/action/browse/about.html
|
|
123
|
+
- lib/miga/cli/action/browse/dataset.html
|
|
124
|
+
- lib/miga/cli/action/browse/dataset_menu_item.html
|
|
125
|
+
- lib/miga/cli/action/browse/datasets.html
|
|
126
|
+
- lib/miga/cli/action/browse/favicon-32.png
|
|
127
|
+
- lib/miga/cli/action/browse/index.html
|
|
128
|
+
- lib/miga/cli/action/browse/layout.html
|
|
129
|
+
- lib/miga/cli/action/browse/redirect.html
|
|
130
|
+
- lib/miga/cli/action/browse/style.css
|
|
121
131
|
- lib/miga/cli/action/classify_wf.rb
|
|
122
132
|
- lib/miga/cli/action/console.rb
|
|
123
133
|
- lib/miga/cli/action/daemon.rb
|